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Action/Adventure

In Zelda II: The Adventure of Link, you can go to Darunia and climb on top of houses. If you go to a roof nearest the top of the screen, you can jump off-screen with the JUMP spell, then (while still off-screen) use the FAIRY spell and fly up. You'll get the animation for falling down a hole and end up in a DIFFERENT town. The villagers all provide game info not found anywhere else in the normal towns. If you exit under the overpass to the right, you'll end up in the middle of the ocean, not being able to move in any direction. If you exit to the left, you'll just end up outside Darunia.

Tomb Raider III has a secret level accessed by finding every (well, technically, all but one, due to an oversight) secret. It appears to have been intended to be a normal level (and showed up in various previews of the game) at first but was cut for some sort of progression reason.

The Tomb Raider IIGaiden Game Golden mask also has a (very wacky) secret level accessed by finding all the secrets in the previous levels.

Tomb Raider: Anniversary has the "style units" gained after finding most of the secrets. Not really a level, as it is just an explorable visual demonstration, but it shows off various experimentations with the art-style of the game and locations.

Toe Jam And Earl has one of the most puzzling floors in the game: Floor 0. How do you get to it? By swimming to a far, far away island in the 1st level of the game. Guide Dang It!!

Action Game

Rolling Thunder 3 for the Genesis has Rounds A-C (one of them being a Nostalgia Level) that serves to substitute the two vehicle stages (Round 3 and 6), as well as the Hijack stage (Round 9), while keeping all of their current weapons and ammo.

Syphon Filter: The Omega Strain's secret missions are unlocked by completing each block of missions within par time with all of the objectives accomplished.

First-Person Shooter

Pretty much every early 2.5D FPS (and 3D, with Quake) has a secret level at some point or other, whether it's once an episode or just one or two in the whole game. They are usually accessed by using a hidden, secret exit on a level rather than the regular exit.

Doom II had two secret levels set in levels taken from Wolfenstein 3D, with one accessed from a secret exit found in the other. The second one required you to kill four clones of Commander Keen hanging from a noose to access the exit.

Descent had some secret levels late in the game. They were difficult, but you could be rewarded with a lot of points and some weapons upgrades.

Wolfenstein 3D itself had a secret level in a gigantic maze where you collect bonus orbs for high score where you're beset upon by four ghosts. Four giant colourful ghosts. With googly eyes. Yes. It's a level of Pac-Man.

The Aztec and Egyptian levels in GoldenEye (1997). The former deals with the Drax Corporation from Moonraker, and the latter has Baron Samedi, who somehow procured the Golden Gun and is taunting MI-6 with it (that level doesn't make a whole lot of sense story-wise, come to think about it). The levels carry their own unique challenges: the Drax soldiers have an over-reliance on grenades which sharp-shooting players can turn against them, and the Egyptian tomb has a Guide Dang It! method of getting the Golden Gun.

The "Panzerknacker Unleashed" missions in Medal of Honor Underground. They are based on multiplayer maps from the previous game, and they are very, very hard.

Level 4-0 in Medal of Honor: Allied Assault is accessible only through the console, and looks like it was supposed to be part of Mission 3, but was Dummied Out for progression/pacing reasons. There's also the Bazooka-Med bonus level accessed by earning the medal on Sniper's Last Stand.

The BloodGame ModDeath Wish for Blood, which places great emphasis on making level transitions logical, puts a spin on this — each secret level is followed by revisiting a fragment of the previous map, where the player has to face a single tough fight (usually a boss and his flunkies) before he can head to the regular exit to resume normal level progression.

The secret levels in Perfect Dark are markedly different from those in Goldeneye mentioned above. Instead of brand-new levels with no plot significance, they're retreads of previous levels from a different point of view, which reveal different parts of the story. The first one shows how an alien Mookkidnapped the CEO of dataDyne (she was later killed aboard the ship) and imploded the building, effectively destroying the company. The other two missions let you play as the grey aliens, one where Elvis alerts the Institute of being captured by Area 51 and you play through the entire level with diminished health, and the other has you play as a soldier among a platoon who landed on the planet after Joanna dropped the shields. Both missions are insanely difficult.

Marathon Infinity: Blood Tides of Lh'owon has several of these, which are either alternate endings where the W'rkncacnter destroy the universe, or "co-op carnage break" levels that can (or are supposed to) only be accessed in multiplayer mode. Then there's the three Vidmaster's Challenge levels, found via a secret exit on the final stage.

The best-hidden secret level is "Hats off to Eight Nineteen," which can only be reached by noting down strings of hex code found on terminals in the first and last levels, copying them into a text file and unzipping the file twice, whereupon it turns into a map file you can load in the game.

Nitemare 3D goes straight from level 4 to level 6 if you play it normally. Or, you can simply push a bunch of boxes in front of one of a pair of dumbwaiters (which will otherwise just transport you back and forth) and get in the other to jump to level 5, which is full of gun-wielding human enemies.

Hack & Slash

The secret Cow Level in Diablo 2, which was made after various rumours about one in the original Diablo.

Diablo III has Whimsyshire, a land that seems ripped straight from Care Bears with smiling clouds, purple bears and unicorns. It can only be accessesd by completing a recipe, or killing a Rainbow Goblin. A later patch also added Greed's Domain, which is a rare portal that opens after killing Treasure Goblins. It features a unique boss and has pots that literally drop millions of gold pieces. Being lucky enough to enter one pretty much ensures you'll never have to worry about money ever again.

Pinballs

Entering a cheat code in Last Gladiator gives access to a secret "Victors" table.

Platform Games

Prinny: Can I Really Be the Hero? and it's sequel has this. Considering that this is that kind of game, they also count as a Brutal Bonus Level. In the sequel, you have to collect a set amount of dolls and it's a lot easier said than done. Thankfully enough, these levels set your lives at infinite, unfortunately, your device and sanity weren't considered.

Legend of Grey Moon has a number of well-hidden secret rooms; these are typically much easier than the rooms that make up normal areas, if not totally harmless, and most of the time are either silly jokes or completely meaningless. Particularly interesting are one level made of Epileptic Flashing Lights which is reached through a secret passage in another secret room, another containing a secret seventeenth gem, and the Special Thanks To room, a Developer's Room of sorts.

Wario Land; almost every game in the series has many secret levels, including whole secret worlds.

Super Mario World 2 (Yoshi's Island) had one secret level per world (accessed by 100% completion of the normal levels), generally based around a gimmick, much harder than other levels, or both. The Game Boy Advance remake has another secret level per world once the game has been beaten.

Luigi's Mansion has multiple hidden, secret or otherwise unneeded rooms inside the game, which are essential for 100% completion and getting all of the ghosts, but is often entirely optional and one may even forget to do them while playing because those rooms are never mentioned.

... For instance, there's the hidden area within the Unbearable level, where you need to jump into a seemingly bottomless pit in order to gain access to a hidden area within the level, which swaps the level theme from a towards the screen chase sequence to a side scrolling section.

...On another level, the player has to jump on what looks like a conspicuously static stack of Nitro crates to teleport to a secret section and get the purple gem.

... Then there are the levels which you need to unlock by finding secret bonuses in other levels, such as standing on a hard to get to platform, or jumping over a long hole to get back to the polar bear, in order to unlock hidden levels, and alternate paths in other levels.

Crash Bandicoot 3: Warped does the same once again in accessing hidden levels with alternate routes, but makes you beat time trials to get to them. However, there are still two hidden levels not at all required for 100% completion, but required for 105% completion. While all of the secret levels in Crash 2 can be found without a guide with enough persistence, Crash 3's secret levels are really obscure. One of them has you driving into a sign on the side of the road in a motorcycle level.

In Mega Man X3, there's a secret level that can only be accessed through specific teleportation capsules, that take you to an abandoned factory where you can fight Vile, The Dragon of the first game. Finding and beating him will result in another boss appearing in his stead later on, where he would normally find and attack you.

Then, in Mega Man X6, there's a secret "Nightmare Stage" for every normal level, where you can find secret upgrades and bosses.

Roll Away has two kinds of secret level; trippy Bonus levels reached upon collecting five friuts where you have to hit every block, and regular levels IN SPACE reached from secret exits.

World 8, Sky Roost in HarmoKnight, which is unlocked after collecting 5 Tori Birds, is an entire Secret Level merged into one big world. It tries to mimick the earlier worlds, but (as the princess says) puts a twist on them. These eight levels look like normal levels, but then you enter one of the levels, and see thousands of Mooks, Spikes of Doom, and Bottomless Pits. You get the sudden realization that the princess told you these levels are Nintendo Hard. Final Trial is just simply a gigantic death trap.

Kid Chameleon has many levels named "Elsewhere". All of them are technically secret levels. Early on, they generally have to be discovered and act as shortcuts, but later in the game, there are plenty that can accidentally be accessed and lead backwards (or just through to a different path of levels).

Skyblazer had a series of secret stages hidden on the overworld map- by going to one of the completed stages and pressing up on the D-pad you'd go to one of the Mode 7 flying bonus stages, which would lead to a secret hut where you could get the game's hidden life upgrade. To get back to the main game and continue with your adventure you had to complete a short 1-screen stage called 'Ship to Nowhere', where you ride a small wooden boat across the lake and have to avoid being washed overboard by huge waves while fighting off the enemies the waves deposit on the deck. Survive all the waves and the stage simply ends, depositing you behind the Lair of Kharyon.

Each level has areas accessible only with the use of red wormholes (which appear temporarily if you step onto a specific tile) and secret switches (which make parts of the terrain change temporarily).

Additionally, it seems that the game was intended to also have actual secret levels. They would be unlocked if a grunt carrying a specific tool (most likely one that is impossible to get on the main level without cheats) steps on a specific tile. However, only one such level made it into the game.

Real-Time Strategy

StarCraft: Brood Wars featured a secret mission which hinted at a major plot point in the sequel. It had no lasting impact on the game otherwise. Said sequel also features a hidden mission in the Terran campaign.

Similarly, Warcraft III: The Frozen Throne had a hidden tower defense mini-game. If you defeated all the waves, you would receive a bonus hero in the following level.

Age of Empires II has a level based on the Saxon Revolt hidden in the files. It must be imported into the game by following instructions provided by the Read Me.

Rhythm Games

Cytus has a number of hidden songs, which are unlocked by interacting with the splash screens of non-hidden songs. Many of these will require a guide or some trial-and-error to discover. They will count towards your chapter and game score and songs cleared totals (in fact, playing every non-hidden song and seeing that the "songs cleared" counter isn't maxed out for that chapter is a giveaway that hidden songs exist), as well as your TP average, but you won't be able to see your records for these songs. The chapter select itself also has hidden songs, triggered by tapping on the Easy and Hard song clear counters.

Role-Playing Games

Quest 64 has a secret level in the desert. While in a completely unrelated and skippable area, it does have a ton of powerups which are normally hard to find.

Dark Souls has The Painted World of Ariamas, the Great Hollow, and the Ash Lake. For the most part, they're difficult-to-find Breather Levels with lots of really good loot.

Undertale had Hard Mode, a version of the first area with more difficult-to-spare monsters, activated by giving the fallen human the same name as the player character.

Stealth-Based Games

"Requiem," the final mission of Hitman: Blood Money. When it starts, it appears to just be a screenshot of 47's funeral over which the end credits are actually playing. Twirling the analog sticks (or pressing "W" on the computer) eventually causes 47 to get up, at which point the credits disappear and the mission begins. (This level is so secret that, on the Xbox versions, an achievement is awarded for completing the game after finishing the previous level. Realizing that there is a mission in "Requiem," and then completing it, is good for a second achievement of equal value.)

Sheep, Dog 'n' Wolf has two, both cleverly hidden in the Hub Level. One at the end of a passage in a wall that looks like a completely ordinary wall, and the other accessed by entering one of the doors from the other side.

Star Fox has the Black Hole and Out Of This Dimension, both accessible from the two Asteroid Belt stages.

Tyrian is absolutely chock-full of secret levels. As a rule, they're accessed by destroying a specific target in a level so that a big glowy sphere appears. When you grab it, you'll move on to the corresponding secret level after finishing the current one. Some of these are tough to get, requiring you to leave certain enemies alone or stay on a certain path. There's even secrets 'within' secret levels, so you can go through a bunch of secret levels in a row before returning to the normal ones.

Gradius, as a series, is flat-out obsessed with hidden levels. Most games in the series have a secret alternate path, usually be doing something during the level to change the boss you fight. This gets lampshaded in ReBirth, where you can fight a different boss but end up in the same level 2 stage regardless - the actual Secret Levels (there are three) are much better hidden. Not every game uses hidden stages, but rather Multiple Paths.

The self parody series Parodius makes fun of this along with everything else - the secret levels in some of those games are even more insane than the standard ones.

Wide-Open Sandbox

Saints Row 2 has Revelation, which provides closure to the ending of the first game and is not unlocked through the standard story progression. Instead, you are given a hint to go to the police headquarters, where you can listen to three wiretap conversations and find Dex's phone number, who directs you to the mission start.

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